Development of genomic resources in the domestic cat is key to application of this species as a model for heritable and infectious diseases, and for comparative genome analysis. Previous versions of the cat gene map, based on somatic cell hybrid analysis, revealed considerable conservation of synteny with the human genome. However, these maps provided no knowledge of gene order and genome rearrangement between the two species, information that is critical to applying the comparative candidate approach to positional cloning in gene-poor model systems. Radiation hybrid (RH) mapping has emerged as the most powerful tool for constructing moderate-to high-density gene maps in vertebrates by obviating the need to identify interspecific polymorphisms. A domestic cat RH panel has been developed and serves as the backbone for feline gene mapping, while also serving to cross-reference microsatellite positions on the domestic cat linkage map. We are in the process of completing a fourth generation radiation hybrid map of the cat, which nearly doubles our past cover of the cat genome. The fourth generation map will integrate approximately 1100 Type I coding loci (expressed sequence tags, genes, and comparative anchor tagged sequences [CATS] markers) with 900 microsatellites. Type I marker density has been increased to nearly 1100 loci through additional expressed sequence tag (EST) development and bacterial artificial chromsome (BAC)-end sequencing-based marker production, focusing primarily on gaps in human-cat synteny. Microsatellites will span every autosome with an average spacing of roughly one polymorphic single tandem repeat (STR) every 3.5 centimorgans, and a total marker resolution (Type I and Type II loci) of one locus every 1.6 megabases. The fourth generation map will offer increased resolution of conserved synteny between human and cat or human and dog for fine-scale mapping efforts. Additionally, the map will act as a critical scaffold for the anchoring of sequence contigs that are currently being assembled from the 2X genome sequencing of the cat sponsored by NHGRI. The current feline RH map now incorporates sufficient Type I and Type II markers to facilitate the identification of genes, using comparative candidate positional clone analysis, controlling phenotypes of interest such as those relating to hereditary disease, coat color, patterning and morphology. Over 250 hereditary phenotypes have been described in the domestic cat. These resources can also be extended to the remaining 36 species of the cat family for population genetic and evolutionary genomic analyses. Further refinement of rearrangement breakpoints and conserved segment boundaries will enhance cross-reference to other mammalian species' genomes for use in diverse studies of genetics and genome evolution.